[CP2K-user] [CP2K:16224] Re: How to do metadynamics with CV1 and CV2 and set up restraint using CV3 in cp2k?

[Matt D]

Hi Hongxia,

I guess because you have set DeltaT to 50000K... I'm not surprised the 
atoms fly apart in this case. 

If this is your first metadynamics run, I'd recommend running an unbiased 
simulation first (i.e. not WELL_TEMPERED and no DELTA_T set) and see how 
the CV evolves. You can then set the width of the Gaussians (SCALE) 
according to variations in the value of the CV with time, for example by 
taking the standard deviation of the CV and setting this to be SCALE. Once 
you have set an appropriately sized gaussian, you can then introduce the 
bias. The bias factor is given by (T+deltaT)/T. Given 298K is your starting 
temperature and you were using 50000 as deltaT, your bias factor is rather 
large. A good initial range might be somewhere in the region of 5 or 10 for 
the bias factor, so deltaT around 1000 - 2000 K. Of course this is system 
dependent so you need to try several values, the higher the value the more 
of free-energy space you will explore, though you want to make sure it's 
comparable to the free energy barriers you want to traverse to avoid 
getting situations where you explode the simulation as you have done by 
using 50000K for deltaT.

Best wishes,
Matt

On Wednesday, 20 October 2021 at 00:24:02 UTC+1 hongxi... at gmail.com wrote:

> Dear cp2k users and developers,
>
> I am trying to do a metadynamics in cp2k. I set 3 collective variables. I 
> want to use CV1 and CV2 as collective variables for metadynamics, while at 
> the same time using CV3 for a restraint to constraint the motion of two 
> molecules not too far away from each other. Could anyone help me set this 
> up appropriately? 
>
> My input is as folllows.
> I set up the three COLVAR in SUBSYS section first. 
> &COLVAR 1
>       &COORDINATION
>         ATOMS_FROM 2 3
>         ATOMS_TO 1 4
>         R_0 [angstrom] 1.2
>         NN 8
>         ND 14
>       &END COORDINATION
>     &END COLVAR
>
>     &COLVAR 2
>       &COORDINATION
>         ATOMS_FROM 5 6
>         ATOMS_TO 1 4
>         R_0 [angstrom] 1.2
>         NN 8
>         ND 14
>       &END COORDINATION
>     &END COLVAR
>
>     &COLVAR 3
>       &DISTANCE
>         POINTS 1 2
>         &POINT 1
>           ATOMS 2 3
>           TYPE GEO_CENTER
>         &END POINT
>
>         &POINT 2
>           ATOMS 5 6
>           TYPE GEO_CENTER
>         &END POINT
>       &END DISTANCE
>     &END COLVAR
>
> And then I add the constraint section in the MOTION section.
> &MOTION
>
>  &CONSTRAINT
>   &COLLECTIVE
>     COLVAR 3
>     INTERMOLECULAR .TRUE.
>     TARGET [angstrom] 5.0
>     &RESTRAINT
>       K 100000
>     &END RESTRAINT
>   &END COLLECTIVE
>  &END CONSTRAINT
>
>  &MD
>     ENSEMBLE NVT
>     STEPS  400000
>     TIMESTEP 0.5
>     TEMPERATURE 298.0
>     &THERMOSTAT
>       TYPE CSVR
>       REGION MASSIVE
>       &CSVR
>         TIMECON [fs] 200.0
>       &END
>     &END
>   &END MD
>   &FREE_ENERGY
>     &METADYN
>
>       DO_HILLS
>       WELL_TEMPERED
>       DELTA_T 50000
>       NT_HILLS 30
>       WW 0.005
>
>       &METAVAR
>         SCALE 0.2
>         COLVAR 1
>       &END METAVAR
>
>       &METAVAR
>         SCALE 0.2
>         COLVAR 2
>       &END METAVAR
>
>       &PRINT
>         &COLVAR
>            COMMON_ITERATION_LEVELS 2
>            &EACH
>              MD 1
>            &END
>         &END
>         &HILLS
>            COMMON_ITERATION_LEVELS 2
>            &EACH
>              MD 1
>            &END
>         &END
>       &END
>     &END METADYN
>   &END FREE_ENERGY
>
> Does anyone know what I did wrong and how to set it up appropriately 
> instead? With this input, I got super huge potential energy and then the 
> geometry fly away.
>
> Thanks in advance!
>
> Sincerely
> Hongxia
>
>
>

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